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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

A structural explanation for the mechanism and specificity of plant branching enzymes I and IIb

Branching enzymes (BEs) are essential in the biosynthesis of starch and glycogen and play critical roles in determining the fine structure of these polymers. The substrates of these BEs are long carbohydrate chains that interact with these enzymes via multiple binding sites on the enzyme’s surface. By controlling the branched-chain length distribution, BEs can mediate the physiological properties of starch and glycogen moieties; however, the mechanism and structural determinants of this specificity remain mysterious. In this study, we identify a large dodecaose binding surface on rice BE I (BEI) that reaches from the outside of the active site to the active site of the enzyme. Mutagenesis activity assays confirm the importance of this binding site in enzyme catalysis, from which we conclude that it is likely the acceptor chain binding site. Comparison of the structures of BE from Cyanothece and BE1 from rice allowed us to model the location of the donor-binding site. We also identified two loops that likely interact with the donor chain and whose sequences diverge between plant BE1, which tends to transfer longer chains, and BEIIb, which transfers exclusively much shorter chains. When the sequences of these loops were swapped with the BEIIb sequence, rice BE1 also became a short-chain transferring enzyme, demonstrating the key role these loops play in specificity. Taken together, these results provide a more complete picture of the structure, selectivity, and activity of BEs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Biogenic coal-to-methane conversion can be enhanced with small additions of algal amendment in field-relevant upflow column reactors

Subsurface coal environments, where biogenic coal-to-methane conversion occurs, are difficult to access, resulting in inherent challenges and expenses for in situ experiments. Previous batch reactor studies provided insights into specific processes, pathways, kinetics, and engineering strategies, but field-relevance is restricted due to limited substrate availability or byproduct accumulation that may influence reactions or metabolisms. In this study, continuous-flow column reactors were used to overcome some batch limitations, improve the understanding of in situ conditions, and increase field-relevance for subsurface engineering technology development. The bench-scale reactor system was constructed to investigate the addition of algal amendment for enhancing microbial coal-to-methane conversion previously developed in batch systems. Four reactor columns were packed with coal and inoculated with a microbial consortium from the same Flowers-Goodale coal bed. Two reactors were amended with 13 C-labeled algal amendment on day 0, and two were unamended. On day 61, one previously amended and one previously unamended reactor were re-amended. Produced gases were captured in a gas trap, and CH 4 and CO 2 were quantified. The reactor amended twice produced 1712.6 µmol CH 4 (4.6% as 13 CH 4 ). The reactor amended only on day 0 produced 1485.5 µmol CH 4 (2.6% as 13 CH 4 ). The reactor amended only on day 61 produced 278.9 µmol CH 4 (3.9% as 13 CH 4 ). The reactor with no amendment produced no measurable gases for the duration of the 172-day experiment. Amendment increased the rate of coal-to-methane conversion and total gas production; most of the produced gases were due to coal conversion with only small contributions (<7%) from amendment conversion.

09 BIOMASS FUELS↗
DOE OSTI2023

The structural basis of mRNA recognition and binding by yeast pseudouridine synthase PUS1

The chemical modification of RNA bases represents a ubiquitous activity that spans all domains of life. Pseudouridylation is the most common RNA modification and is observed within tRNA, rRNA, ncRNA and mRNAs. Pseudouridine synthase or ‘PUS’ enzymes include those that rely on guide RNA molecules and others that function as ‘stand-alone’ enzymes. Among the latter, several have been shown to modify mRNA transcripts. Although recent studies have defined the structural requirements for RNA to act as a PUS target, the mechanisms by which PUS1 recognizes these target sequences in mRNA are not well understood. Here we describe the crystal structure of yeast PUS1 bound to an RNA target that we identified as being a hot spot for PUS1-interaction within a model mRNA at 2.4 Å resolution. The enzyme recognizes and binds both strands in a helical RNA duplex, and thus guides the RNA containing the target uridine to the active site for subsequent modification of the transcript. The study also allows us to show the divergence of related PUS1 enzymes and their corresponding RNA target specificities, and to speculate on the basis by which PUS1 binds and modifies mRNA or tRNA substrates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Mechanisms of Manganese(II) Oxidation by Filamentous Ascomycete Fungi Vary with Species and Time as a Function of Secretome Composition

Manganese (Mn) oxides are among the strongest oxidants and sorbents in the environment, and Mn(II) oxidation to Mn(III/IV) (hydr)oxides includes both abiotic and microbially-mediated processes. While white-rot Basidiomycete fungi oxidize Mn(II) using laccases and manganese peroxidases in association with lignocellulose degradation, the mechanisms by which filamentous Ascomycete fungi oxidize Mn(II) and a physiological role for Mn(II) oxidation in these organisms remain poorly understood. Here we use a combination of chemical and in-gel assays and bulk mass spectrometry to demonstrate secretome-based Mn(II) oxidation in three phylogenetically diverse Ascomycetes that is mechanistically distinct from hyphal-associated Mn(II) oxidation on solid substrates. We show that Mn(II) oxidative capacity of these fungi is dictated by species-specific secreted enzymes and varies with secretome age, and we reveal the presence of both Cu-based and FAD-based Mn(II) oxidation mechanisms in all 3 species, demonstrating mechanistic redundancy. Specifically, we identify candidate Mn(II)- oxidizing enzymes as tyrosinase in Stagonospora sp. SRC1lsM3a, bilirubin oxidase in Stagonospora sp. and Paraconiothyrium sporulosum AP3s5-JAC2a, and GMC oxidoreductase in all 3 species, including Pyrenochaeta sp. DS3sAY3a. Furthermore, we demonstrate that secretome-based Mn(II) oxidative capacity is induced by the presence of Mn(II) in Stagonospora sp. and Pyrenochaeta sp., suggesting a physiological role for Mn(II) oxidation in these Ascomycetes. The diversity of the candidate Mn(II)-oxidizing enzymes identified in this study suggests that the ability of fungal secretomes to oxidize Mn(II) may be more widespread than previously thought.

Zeiner, Carolyn A.↗
NASA NTRS1977

Thick-film preamplifier

Preamplifier with hybrid discrete components and integrated-circuit packaging is designed specifically for use as television image-tube output signal conditioner. Circuit is fabricated on alumina substrate, measuring 0.5 by 0.5 by 0.015 inch using gold-base conductor with conductive gold crossovers and dielectric insulation.

Bailey, G. C.↗
NASA NTRS1981

Aspects of the mechanisms of smoke generation by burning materials

An investigation of smoke generation during the burning of natural and synthetic solid materials (relevant to fire safety problems), under simulated fire conditions, is presented. Smoke formation mechanisms, including flaming and nonflaming combustion, are reviewed, and the complex physical, chemical, and electrical processes, important in smoke particulate production, are identified. With reference to the smoke formation mechanisms, measured experimental data are discussed, and include effects of ventilation gas temperature, dependence on material composition, and chemical analysis of smoke particulates. Significant differences in smoke characteristics are observed between flaming and nonflaming conditions, which is attributed to specific differences in controlling mechanisms and resultant ways leading to particulate formation. The effects of polymer substrate properties and effects of additives for a given substrate on smoke properties are also discussed in terms of basic processes. It is shown that many of the measured trends can be interpreted by considering postulated mechanisms of particulate formation.

Bankston, C. P.↗
NASA NTRS2002

The AMPA receptor subunit GluR1 regulates dendritic architecture of motor neurons

The morphology of the mature motor neuron dendritic arbor is determined by activity-dependent processes occurring during a critical period in early postnatal life. The abundance of the AMPA receptor subunit GluR1 in motor neurons is very high during this period and subsequently falls to a negligible level. To test the role of GluR1 in dendrite morphogenesis, we reintroduced GluR1 into rat motor neurons at the end of the critical period and quantitatively studied the effects on dendrite architecture. Two versions of GluR1 were studied that differed by the amino acid in the "Q/R" editing site. The amino acid occupying this site determines single-channel conductance, ionic permeability, and other essential electrophysiologic properties of the resulting receptor channels. We found large-scale remodeling of dendritic architectures in a manner depending on the amino acid occupying the Q/R editing site. Alterations in the distribution of dendritic arbor were not prevented by blocking NMDA receptors. These observations suggest that the expression of GluR1 in motor neurons modulates a component of the molecular substrate of activity-dependent dendrite morphogenesis. The control of these events relies on subunit-specific properties of AMPA receptors.

Non-NASA Center↗
NASA NTRS1999

Left-handed Z-DNA: structure and function

Z-DNA is a high energy conformer of B-DNA that forms in vivo during transcription as a result of torsional strain generated by a moving polymerase. An understanding of the biological role of Z-DNA has advanced with the discovery that the RNA editing enzyme double-stranded RNA adenosine deaminase type I (ADAR1) has motifs specific for the Z-DNA conformation. Editing by ADAR1 requires a double-stranded RNA substrate. In the cases known, the substrate is formed by folding an intron back onto the exon that is targeted for modification. The use of introns to direct processing of exons requires that editing occurs before splicing. Recognition of Z-DNA by ADAR1 may allow editing of nascent transcripts to be initiated immediately after transcription, ensuring that editing and splicing are performed in the correct sequence. Structural characterization of the Z-DNA binding domain indicates that it belongs to the winged helix-turn-helix class of proteins and is similar to the globular domain of histone-H5.

Review↗
NASA NTRS2009

Silicon Nanowire Growth at Chosen Positions and Orientations

It is now possible to grow silicon nanowires at chosen positions and orientations by a method that involves a combination of standard microfabrication processes. Because their positions and orientations can be chosen with unprecedented precision, the nanowires can be utilized as integral parts of individually electronically addressable devices in dense arrays. Nanowires made from silicon and perhaps other semiconductors hold substantial promise for integration into highly miniaturized sensors, field-effect transistors, optoelectronic devices, and other electronic devices. Like bulk semiconductors, inorganic semiconducting nanowires are characterized by electronic energy bandgaps that render them suitable as means of modulating or controlling electronic signals through electrostatic gating, in response to incident light, or in response to molecules of interest close to their surfaces. There is now potential for fabricating arrays of uniform, individually electronically addressable nanowires tailored to specific applications. The method involves formation of metal catalytic particles at the desired positions on a substrate, followed by heating the substrate in the presence of silane gas. The figure illustrates an example in which a substrate includes a silicon dioxide surface layer that has been etched into an array of pillars and the catalytic (in this case, gold) particles have been placed on the right-facing sides of the pillars. The catalytic thermal decomposition of the silane to silicon and hydrogen causes silicon columns (the desired nanowires) to grow outward from the originally catalyzed spots on the substrate, carrying the catalytic particles at their tips. Thus, the position and orientation of each silicon nanowire is determined by the position of its originally catalyzed spot on the substrate surface, and the orientation of the nanowire is perpendicular to the substrate surface at the originally catalyzed spot.

Getty, Stephanie A.↗
NASA NTRS2001

Inexpensive Method for Growing Unidirectional Oriented Materials Using Friction-Transferred Poly(tetrafluoroethylene) Substrates

In recent years, there has been an increasing interest in properties of unidirectional materials grown on highly oriented polymer surfaces such as the poly(tetrafluoroethylene) (PTFE) films coated onto smooth glass surfaces. In this technique, a thin PTFE film is deposited by sliding or rubbing a Teflon bar over a heated glass surface at a specific temperature. Depending on the pressure, temperature and sliding rate the thickness of deposited layers can be varied from 30 A to 150 A. The PTFE-coated substrate is simple yet surprising versatile for oriented growth of many organic, inorganic and polymer. The significant aspect of PTFE films is their unusual ability to molecularly align a wide variety of materials grown onto them from solution, melt or vapor phase deposition, at temperature below the melting point of PTFE (approx. 340 C). The PTFE structure may be derived, in part, from the multitude of ridges forming in the film and these ridges can presumably provide effective nucleation sites to induce the unidirectional growth of variety of materials. Electron diffraction studies of these films revealed that the PTFE macromolecules are oriented parallel to each other along the sliding direction. Direct observation of the film thickness, molecular structure and individual fluorine atoms from these highly oriented films were achieved using atomic force microscopy (AFM). In this paper, we also report the first direct observation of individual fluorine atoms, and the measurement of the fluorine-helix and carbon-helix radii to be 1.70 A and 0.54 A, respectively.

Lee, Jonathan A.↗
DOE OSTI2025

Biosynthesis of bioprivileged, linear molecules via novel carboligase reactions

Over the award period, we made progress on the three aims. We screened twenty-five carboligases for activity coupling twenty-one possible -keto acids (Aim 1). The carboligases were selected across a diverse set of protein sequences. Using Q-Exactive UHPLC-MS, we tested a total of 210 coupled products per enzyme and generated a dataset of 5250 enzyme-substrate activity relationships. We identified multiple enzymes that had activity for synthesizing suberic acid and heptanoic acid (Aim 2). We built a random forest model for predicting the activity of each enzyme toward substrates on which it was not tested using the data from Aim 1. Finally, we evaluated growth defects that occurred due to expression of different carboligases in E. coli (Aim 3). We were able to identify specific metabolites and putative pathways that, when supplemented in the media, recovered the growth defect associated with the presence of specific carboligases. We are in the process of publishing two manuscript describing the methods for high-throughput screening of enzyme promiscuity, using machine learning to predict activity on untested substrates, and enzyme activity data we collected. This project has produced enabling data for biosynthesis of a range of new-to-nature compounds to support biomanufacturing.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Molecular Basis of Broad Spectrum N -Glycan Specificity and Processing of Therapeutic IgG Monoclonal Antibodies by Endoglycosidase S2

Immunoglobulin G (IgG) glycosylation critically modulates antibody effector functions. Streptococcus pyogenes secretes a unique endo-β-N-acetylglucosaminidase, EndoS2, which deglycosylates the conserved N-linked glycan at Asn297 on IgG Fc to eliminate its effector functions and evade the immune system. EndoS2 and specific point mutants have been used to chemoenzymatically synthesize antibodies with customizable glycosylation for gain of functions. EndoS2 is useful in these schemes because it accommodates a broad range of N-glycans, including high-mannose, complex, and hybrid types; however, its mechanism of substrate recognition is poorly understood. We present crystal structures of EndoS2 alone and bound to complex and high-mannose glycans; the broad N-glycan specificity is governed by critical loops that shape the binding site of EndoS2. Furthermore, hydrolytic experiments, domain-swap chimeras, and hydrogen–deuterium exchange mass spectrometry reveal the importance of the carbohydrate-binding module in the mechanism of IgG recognition by EndoS2, providing insights into engineering enzymes to catalyze customizable glycosylation reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRSDate not supplied

Analysis of Bioburden Associated with Nonmetallic Spacecraft Materials

Planetary Protection (PP) requirements help to ensure the integrity of life-detection science conducted on solar system bodies, particularly those with liquid water. Such requirements are often met by a combination of cleaning and verification steps to reduce microbial contamination (i.e. bioburden) to an acceptable limit. There are only two cleaning methods approved by the National and Space Administration (NASA), vapor hydrogen peroxide (VHP) and heat microbial reduction (HMR), the latter of which is the most commonly employed. However, HMR can be harsh and produce its own concerns about material integrity, like aging or increasing hardness. When bioburden reduction methods cannot be employed, the project must rely on assumed NASA specification values of bioburden which can cause compliance issues with strict PP bioburden limitations. This work aimed to more accurately define the risk of contamination of a target body by providing empirical data associated with raw materials commonly used in solid rocket motors for lander missions. In this study, we pulverized nonmetallic materials using a cryogenic grinder, then analyzed the resulting substrate for microbial colony forming units (CFU). We found that many nonmetallic materials do not harbor large bioburden when compared with the NASA specification values, though a range existed depending on the material, treatment, and handling. The results from this work provide quantitative data to help reduce concerns of contamination, while also providing a foundation for follow up studies into additional sterilization methods and molecular identification of contaminating microbes.

Planetary Protection↗
NASA NTRS2008

Final Report on Portable Laser Coating Removal Systems Field Demonstrations and Testing

Processes currently used throughout the National Aeronautics and Space Administration (NASA) to remove corrosion and coatings from structures, ground service equipment and small components results in waste streams consisting of toxic chemicals, spent media blast materials, and waste water. When chemicals are used in these processes they are typically high in volatile organic compounds (VOC) and are considered hazardous air pollutants (HAP). When blast media is used, the volume of hazardous waste generated is increased significantly. Many of the coatings historically used within NASA contain toxic metals such as hexavalent chromium, and lead. These materials are highly regulated and restrictions on worker exposure continue to increase. Most recently the EPA reduced the permissible exposure limit (PEL) for hexavalent chromium. The new standard lowers OSHA's PEL for hexavalent chromium from 52 to 5 micrograms of Cr(V1) per cubic meter of air as an 8-hour time-weighted average. Hexavalent chromium is found in the pretreatment and primer coatings used within the Shuttle Program. In response to the need to continue to protect assets within the agency and the growing concern over these new regulations, NASA is researching different ways to continue the required maintenance of both facility and flight equipment in a safe, efficient and environmentally preferable manner. The use of laser energy to remove prepare surfaces for a variety of processes, such as corrosion and coating removal, weld preparation and non destructive evaluation is a relatively new technology that has shown itself to be environmentally preferable and in many cases less labor intensive than currently used removal methods. The development of a Portable Laser Coating Removal System (PLCRS) started as the goal of a Joint Group on Pollution Prevention (JG-PP) project, led by the Air Force, where several types of lasers in several configurations were thoroughly evaluated. Following this project, NASA decided to evaluate the best performers on processes and coatings specific to the agency. Laser systems used during this project were all of a similar design, most of which had integrated vacuum systems in order to collect materials removed from substrate surfaces during operation. Due to the fact that the technology lends itself to a bide variety of processes, several site demonstrations were organized in order to allow for greater evaluation of the laser systems across NASA. The project consisted of an introductory demonstration and a more in-depth evaluation at Wright-Patterson Air Force Base. Additionally, field demonstrations occurred at Glenn Research Center and Kennedy Space Center. During these demonstrations several NASA specific applications were evaluated, including the removal of coatings within Orbiter tile cavities and Teflon from Space Shuttle Main Engine gaskets, removal of heavy grease from Solid Rocket Booster components and the removal of coatings on weld lines for Shuttle and general ground service equipment for non destructive evaluation (NDE). In addition, several general industry applications such as corrosion removal, structural coating removal, weld-line preparation and surface cleaning were evaluated. This included removal of coatings and corrosion from surfaces containing lead-based coatings and applications similar to launch-structure maintenance and Crawler maintenance. During the project lifecycle, an attempt was made to answer process specific concerns and questions as they arose. Some of these initially unexpected questions concerned the effects lasers might have on substrates used on flight equipment including strength, surface re-melting, substrate temperature and corrosion resistance effects. Additionally a concern was PPE required for operating such a system including eye, breathing and hearing protection. Most of these questions although not initially planned, were fully explored as a part of this project. Generally the results from tesng were very positive. Corrosion was effectively removed from steel, but less successfully from aluminum alloys. Coatings were able to be removed, with varying results, generally dark, matte and thin coatings were easier to remove. Steel and aluminum panels were able to be cleaned for welding, with no known deleterious effects and weld-lines were able to have coatings removed in critical areas for NDE while saving time as compared to other methods.

Rothgeb, Matthew J.↗
DOE OSTI2020

A new pinnotherid crab of the genus Pinnixulala Palacios Theil, Cuesta & Felder, 2016 from uncertain infaunal hosts in the northern Gulf of Mexico, with a rediagnosis and updated synonymy for the polychaete symbiont Pinnixulala retinens (Rathbun, 1918) (Decapoda: Brachyura: Pinnotheridae)

Abstract A new infaunal pinnotherid crab, Pinnixulala heardin. sp., is described from muddy substrates of the middle to inner continental shelf of the northern Gulf of Mexico. Molecular genetic analysis supports its separation from P. retinens (Rathbun, 1918), the only other western Atlantic member of the genus and a species most commonly found living as a symbiont of large polychaete worms. Both western Atlantic species are clearly separated from several described and undescribed populations of congeners occurring along shorelines of the eastern Pacific. We herein include a rediagnosis of P. retinens to facilitate morphological comparisons with P. heardin. sp. Unlike P. retinens, which is more common in shallow inshore waters and reaches larger sizes, the new species lacks development of a strong distally directed spine on the fourth pereopod ischium and has chelae that are at least as heavily developed as the second and third pereopods. In addition, the mature male first gonopods in P. heardin. sp. are tapered over their terminal one-third and directed distally, rather than being curved in their terminal one-third with the tips directed mesially, as they are in P. retinens. The new species is invariably collected from samples including infaunal worms and other invertebrates, but the specific hosts remain to be determined

Marine & Freshwater Biology↗
DOE OSTI2021

Determining the Three-Dimensional Structures of Silica-Supported Metal Complexes from the Ground Up

The immobilization of molecularly precise metal complexes to substrates, such as silica, provides an attractive platform for the design of active sites in heterogeneous catalysts. Specific steric and electronic variations of the ligand environment enable the development of structure–activity relationships and the knowledge-driven design of catalysts. At present, however, the three-dimensional environment of the precatalyst, much less the active site, is generally not known for heterogeneous single-site catalysts. We explored the degree to which NMR-based surface-to-complex interatomic distances could be used to solve the three-dimensional structures of three silica-supported metal complexes. Furthermore, the structure solution revealed unexpected features related to the environment around the metal that would be difficult to discern otherwise. This approach appears to be highly robust and, due to its simplicity, is readily applied to most single-site catalysts with little extra effort.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗